This is the first year of operation of the Systems Neuroscience Imaging Resource (SNIR). Much of the focus has been on equipment acquisition and procedure development. The first piece of equipment specifically purchased for the SNIR is a Zeiss AxioscanZ1 slide scanning microscope. This is a high quality widefield microscope with transmitted brightfield and fluorescent epi-illumination capacity. Its most significant feature is the ability to program multichannel tiled acquisition of large areas from up to 100 microscope slides. It is being actively used by investigators from 10 different intramural laboratories for projects that include whole brain mapping of gene expression profiles and the projections of genetically tagged and fluorescently labeled neuron populations. The SNIR has taken on management of a shared Zeiss LSM780 microscope. This instrument is approximately 4 years old. It is a high quality inverted confocal microscope with 405, 488, 514, 561, 594 and 633 nm lasers, a 32-channel spectral detector and 2 conventional PMTS. It is generally used to capacity during core working hours by investigators from approximately 10 different NIMH intramural groups. Acquisition of additional microscopes aimed at systems neuroscience and whole brain imaging is planned. These include an upright confocal/multiphoton microscope and a light sheet microscope. Renovation of space to accommodate this equipment is planned. Microbrightfield Brainmaker and Neurolucida 360 software packages have been acquired to facilitate reconstruction and analysis of systems neuroscience data. Additional software purchases are under investigation. Protocols for multiplex in situ hybridization are being developed and work toward implementation of established protocols for clearing and imaging thick pieces of brain tissue is underway.